MATADOR is a resource for protein-chemical interactions. It differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interacton. The manually annotated list of direct (binding) and indirect interactions between proteins and chemicals was assembled by automated text-mining followed by manual curation. Each interaction contains links to PubMed abstracts or OMIM entries that were used to deduce the interaction. (These articles are not necessarily useful review articles.)
Indirect interactions are caused by many different mechanisms. For example, binding a metabolite of a drug as well as changes in gene expression fall under that category. In order to capture as many interactions as possible, all the different mechanisms are grouped together. You as the user can decide if you rather trust only the direct interactions (with a known mechanism) or also indirect interactions.
How to cite
Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R.
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22. Epub 2007 Oct 16.
- SuperTarget, containing a superset of MATADOR and more analysis options
- DrugBank, another manually annotated list of interactions
- PDSP Ki database, with lots of binding constants
The interactions contained in MATADOR are available for download for non-commercial purposes (419 kB). This file contains the following information, as noted in a header line:
- chemical_id: The PubChem compound identifier. Note that stereoisomers have been merged into one record.
- chemical_name: An automatically picked name of the chemical.
- atc: The ATC Code as defined by the WHO.
- protein_id: A protein identifier, either corresponding to genes from STRING 7 or to a group of genes from MeSH.
- protein_name: The preferred name of the protein.
- mesh_id: If an interaction for a protein was derived via a MeSH term, it is given in this column.
- uniprot_id: UniProt identifiers for the protein.
- protein_score: A score for the confidence in the interaction. 950 ("95%") is the (arbitrary) highest value, which is used for individually derived annotations.
- protein_annotation: The actual annotation, if the interaction was annotated directly for a protein.
- mesh_score: Interactions derived from MeSH terms receive lower scores, depending on the diversity of the protein sequences belonging to the MeSH term.
- mesh_annotation: The actual annotation, if the interaction was found via a MeSH term.
- matador_score: The maximum of the two previous scores.
- matador_annotation: The annotation belonging to said maximum.
If you wish to use MATADOR commercially, please contact Peer Bork to obtain a license.